And Then the Physicist Fell in Love With the Waitress
by superwholockfan
Summary: Leonard and Penny are over. He's back with Leslie. She's somehow become best friends with Sheldon. But Sheldon has been feeling odd around Penny. Could it be...love? Does Sheldon love Penny? Does Penny love Sheldon?
1. Chapter 1

**Disclaimer: I own nothing recognizable.**

**Author's Note: REVIEW! Pretty please!**

Sheldon Cooper sat on his spot, thinking about change. More specifically, a change that had occurred without his knowledge or consent.

Sheldon Cooper was a man of routine, to say the least.

Every minute of his day, pretty much every minute of his existence was planned out. Until a certain actress/waitress came along and disturbed it all.

Suddenly, Sheldon found himself with four friends, three. He sat there, wondering when he began to plan things so Penny would be included. He had never done that. Howard and Raj came with Leonard and without them Sheldon had no one. He didn't need Penny.

But somehow, she had become an instrumental part of his life. Leonard had slipped out of the role of best friend and she had slipped in. They had fallen into an easy routine. It was almost effortless. She accompanied the guys on their excursions to the comic book store and was beginning to qualify as a "nerd". He didn't mind having her around anymore. She woke up every day on Saturday to eat cereal with him and watch Doctor Who. He was allowed to organize her apartment once a week. She was allowed to take him somewhere spontaneously once every three weeks. Yes, they were most definitely best friends.

But something about their relationship perplexed him. He started feeling odd whenever she came over. His pulse would race and his hands would start to prespire. He would feel a bit nauseous and his face would twitch. He had never felt like this.

He stood from his spot when he heard the phone ring. "Hello." he said

"How's my Shelly doing? I was just calling to let ya know I'm coming to see you." His mother said brightly from the other end.

Sheldon sighed, then brightened. Maybe she could help with this...feeling. "When will you be arriving Mother?"

"Tomorrow at about two. Will you have Leonard or that charmin' girl from across the hall come pick me up? What was her name? Patty?"

"Penny will be there to pick you up. Goodbye mother."

"See ya tomorrow, Shelly."

He hung up, still thinking about Penny. Speaking of whom, said waitress walked into the apartment, ready for a Superman movie marathon. Sheldon felt his heart rate pick up when she smiled at him. 'What on earth is happening to me?' Sheldon thought as they started the first movie.


	2. Chapter 2

**Disclaimer: If I owned the Big Bang Theory, it would be all Penny/Sheldon and Raj/Howard. Sadly, I don't.**

**Author's Note: New chapter! Thank to those who took the time to review! There will be some Howard/Raj in this chapter and some Leonard/Leslie!**

Penny smiled at Sheldon as she walked into his and Leonard's apartment. Sheldon glanced at her and nodded as he sat down. She sat down next to him. He looked so darn cute in his Superman t-shirt.

'Woah, where the frack did that come from?' Penny thought. She took another look at him. He did look cute, she decided. Almost...hot.

"Penny." Sheldon said, rousing her from her thoughts.

"What's up, sweetie?"

"My mother is coming to town tomorrow and seeing as I don't drive, would you mind picking her up from the airport?" Sheldon asked.

Penny gave him a warm smile and could have sworn she saw him blush. "Of course I'll pick her up sweetie. What time?"

"She said her plane would be arriving at two."

"Okay, Sheldon. I'll be there." Penny smiled again and this time she definitely saw a blush. Did Sheldon have...a crush on her? No, no fracking way. This was Sheldon Cooper. He was practically a robot. He didn't get crushes.

'What if he does like you? How do you feel about him?' She thought. She decided to try an...experiment. Just to see if Sheldon liked her. She leaned her head on Sheldon's shoulder.

The physicist stiffened, but didn't push her off. Penny laced her fingers through his and he didn't pull away. 'Okay, time to kick things up a notch.' Penny thought.

She wrapped her arms around his waist. Then he really shocked her. Sheldon wrapped his arms around her. They were snuggling! Penny looked up at him. He was staring at her, not paying attention to the movie.

Penny reached her head up. He was leaning towards her and their lips met in the middle.

Penny pulled away. "I...uh...gotta go." She fled the apartment. Once out in the hall, she leaned against the wall. Howard and Raj were coming up the stairs hand in hand. Howard kissed Raj on the lips, not noticing Penny.

"Holy crap on a cracker." Penny said. Since when were they in a relationship?

"Penny! Uh...why aren't you inside?" Howard said, blushing. Raj looked at his shoes, unable to say anything.

"Sheldon kissed me!" The blonde blurted out.

"What? Sheldon? Was he drunk?" Howard said, shocked.

"No! And I kissed him back!" She said, almost crying now. Why had she screwed everything up? She didn't want to lose her whack-a-doodle! Wow, when did he become hers?

"Do you like him?" Raj said, his voice barely above a whisper. Penny looked at him, shocked. "Oh, ever since Howard and I... Well now I can talk to women." He explained, blushing again. Howard wrapped an arm around his shoulders.

"That's the problem! I think I do like him!" She said, crying now. Penny knew it was the truth. Sheldon was neurotic, obsessive, and controlling but he was hers. She loved him.

"Well, I see the way he looks at you. He loves you. It's obvious." Raj said quietly.

"Raj, what am I going to do?" She cried. Raj stepped away from Howard and caught her as she fell.

"Penny, you have to tell him." Raj whispered in her ear.

She let go of Raj. "I know. So, when did you become a couple?" She said.

"Oh, about a month now. Right, Raj?" Howard said.

"Right. Sorry for not telling you. We didn't want anyone to know." Raj said apologetically.

"It's all right. Well, I gotta go." Penny ran into her apartment, almost blinded by tears. How could she be so stupid? She realized now it had never been Leonard. It was always Sheldon.

Sheldon. How had she been so blind? He had always been there for her. Leonard hadn't. Now she had embarrassed herself and potentially destroyed two friendships that night.

When she had broken up with Leonard, it broke his heart. Penny knew it was the right decision, but it hurt to see him like that. That was about two months ago. Now he was with Leslie but she knew he still had feelings for her. She would have to talk to him.

Oh, crap! She had to pick up Sheldon's mom tomorrow! Maybe she should call and...no. She had to face Sheldon eventually. Might as well be sooner rather than later.

Penny went to bed, feeling exhausted and drained. She flopped onto her bed, not even bothering to change her clothes. Penny fell asleep, hoping things would be better in the morning.


	3. Chapter 3

**Disclaimer: If I owned The Big Bang Theory, it would be all Penny/Sheldon and Raj/Howard. Sadly, I don't.**

**Author's Note: This is Sheldon's reaction to the kiss. Review please!**

Sheldon sat frozen on the couch. He kissed Penny. More shockingly, he had not been repulsed by it. In fact it had been kind of...nice.

Raj and Howard walked in. "Hey Sheldon." Howard said.

Sheldon didn't respond. He was in shock. Penny and him had kissed! KISSED. Dr. Sheldon Cooper had never kissed anyone before!

"Dude, what's wrong?" Raj asked.

Sheldon just got up and walked to his room. He didn't have the energy to deal with them tonight. He closed the door and sat down on his bed. Why had Penny run away? He had nothing to compare it to, but he thought it was good. Was he really that bad a kisser?

'Maybe it's you.' Sheldon thought. He knew he was hard to deal with. Most people couldn't stand him. His own friends barely tolerated him. Penny...well he thought she was different. She seemed to actually like him. He thought she may have had a crush on him. Obviously he'd been mistaken. She was just like everyone else.

No. She wasn't like everyone else. Penny was...special. She was always there for him. She was nice to him. Leonard and the others were not. They insulted him and it hurt. He faked indifference, but it hurt. He couldn't help being this way.

Raj walked in."Sheldon, are you okay?"

"You're in my room. No one is allowed in my room." Sheldon replied stiffly.

"This is about you and Penny. I know you two kissed." Raj stated, not leaving the room.

Sheldon didn't say anything. He didn't want to listen to their teasing. It was hurtful.

"Look, dude, I saw Penny in the hallway. She likes you, I can tell." Raj said quietly. The Indian walked out.

Penny...likes him? But why did she run out? Sheldon shook his head. He had never felt this many emotions. Sheldon sighed and walked out of his room.

Raj and Howard were sitting on the couch. They didn't hear Sheldon approaching. Howard wrapped an arm around Raj's shoulders. Raj leaned in and kissed Howard. Howard whispered something in Raj's war and Raj laughed.

Sheldon froze. His breath caught in his throat. 'Oh, frickety frack' Sheldon thought. He walked into the living room.

"In case you were wondering, I'm going to have to tell Leonard about this." Sheldon said loudly.

Howard and Raj broke apart. "Sheldon! What the hell?"Howard yelled.

"I came out of my room. If you two wanted your relationship to remain a secret, you should not have been cuddling on my couch. In my spot." Sheldon stated.

Howard sighed and he and Raj scooted over. "So, everyone knows now." Raj said.

"Penny doesn't." Sheldon said as he sat down.

"Yeah she does. She caught us kissing in the hallway." Howard said. "Eh, it's about time people found out. I'm getting tired of sneaking around."

"Me too." Raj said. "I want to be able to hold your hand in front of our friends. Or kiss you when I have to leave."

Howard looked at Sheldon warily. "I'm guessing you have something annoying and rude to say on the subject of gay relationships."

Sheldon was hurt. He was many things, but not discriminatory. He didn't care what his friends liked. "I don't. I'm glad...glad you're happy." Sheldon said.

Raj and Howard looked surprised. "Really? Thanks, Sheldon." Howard said.

"Let's start the movie." Sheldon said, not looking at the two of them. He was still quite confused about his feelings for Penny and a little shocked about Howard and Raj. He restarted the first Superman movie and tried to pay attention. Leonard came back from his date with Leslie.

"Hey." Leonard said brightly.

"Howard and Raj are in a relationship and Penny kissed me." Sheldon blurted out. He really was terrible at keeping secrets.

"What?" Leonard squeaked.

Sheldon ran back to his room. He laid down on his bed. What had he done? Sheldon didn't leave his room again that night.

**Author's Note: Mary Cooper will be appearing in the next chapter! I promise!**


	4. Chapter 4

**Disclaimer: I own nothing recognizable.**

**Author's Note: Important Author's Note at the end! Please review!**

Penny awoke the next morning to a knocking at her door. She groaned and looked at the clock. 9:30. She pulled herself out of bed and stumbled to the door. She opened it and blinked when she saw Leonard standing there.

"Hi Penny. Can I come in?" Leonard said.

"Umm...sure Leonard." Was all Penny could muster. She'd barely spoken to Leonard since their break up. They saw each other almost every day, with her hanging out with the guys and all, but she mostly talked to Howard and Sheldon. Since he had gotten back together with Leslie, she hadn't even seen him.

"So...how was last night?" Leonard asked, taking a seat on the couch.

Penny could tell he knew about the kiss. "Just say what you came here to say, Leonard."

"Okay. So, you, uh, kissed Sheldon?"

"Yes, Leonard, I did." Penny responded calmly.

"Sheldon? Penny, why? You could do so much better." He took her hand. "Penny, what if you and I gave it another try? I'd treat you better than Sheldon. Give me a chance, Penny." Leonard begged.

Penny was almost crying. She wanted to say yes. Let Leonard love her and give her his heart. But she couldn't. Her heart belonged to a different physicist. "Leonard, I can't. It was never you. I'm sorry, but I...I'm in love with Sheldon. I can't pretend to love you. It would just hurt you and me."

Leonard face blanched. "You...love...him?" He choked out.

"Yeah, I do." She replied.

Leonard took a deep breath."I can see he loves you too. Will you be happy Penny?" Leonard asked.

She thought for a moment. "Yeah, Leonard. I will be."

"Then I'm okay with this." Leonard said.

Penny smiled at him. "Thanks, Leonard. Leslie's a very lucky girl."

Leonard smiled and got up to leave. "Hey, Leonard?"

"Yeah, Penny?"

"I miss you." The blonde whispered.

"I miss you too." Leonard gave her a quick hug and walked out. Penny smiled. Maybe this was the first step to repairing their friendship.

Later that day, Penny arrived at the airport to pick up Sheldon's mother, Mary Cooper. Penny was a little nervous. Mrs. Cooper could always tell what others were feeling. She was definitely going to know something was up between Sheldon and Penny. Just then, Mrs. Cooper walked out of the airport.

"Hi, Mrs. Cooper!" Penny said, taking one of the woman's two bags.

"Penny, please. Call me Mary." The older woman said in that Texas twang of hers. Penny and her climbed in the car and drove off.

"So, what is it about my son that has you head over heels for him?" Mary said after about five minutes of chatting about Sheldon.

Penny sighed. She hadn't expected Mary to work it out that quickly. "How did you know?" Penny asked.

"Let's just call it mother's intuition. Now, tell what my son has done to get you so in love with him." Mary ordered.

Penny didn't really know how to answer. "I guess...he did it by being Sheldon. He's not easy to live with, that's for sure, but he's sweet. He's my best friend."

Mary looked thoughtful. "Well, the way Shelly talks about you, I can almost certainly say that he loves you too. Now, I thank God everyday for blessing me with such a...special boy, but he sure can be stubborn. He probably doesn't know what he's feelin' or he just won't admit it."

Penny almost laughed. Mary could break down her son like no one else. "I know he feels, but I'm not sure what he feels. He's difficult, but I can handle that. He even...kissed me." Penny whispered the last sentence.

Mary laughed. "My little Shelly had his first kiss! Oh Lord, thank you! I thought this day would ever come! That settles it, Penny. He would never kiss anyone unless he was absolutely, completely, head over heels in love."

Penny smiled. "Well, that makes me a very lucky girl." The two women arrived at the apartment building and went inside.

Penny used her key to let herself into the guys' apartment. Sheldon was working on his computer. Penny's heart did a little tap dance when she saw him. He was just so handsome!

"Hello Mother, hello Penny." Sheldon said as he stood up.

"Hi Shelly!" Mary said. She didn't try and hug Sheldon. She knew her son too well to try.

"Well, I have to go. Bye Sheldon, bye Mary." Penny said.

"Wait, darlin'. Won't you stay and chat for a while?" Mary said.

"Yes, Penny, please don't go. You didn't show up for Doctor Who this morning. I didn't watch it. I recorded it so we could watch it together." Sheldon said.

Penny gaped at him. He'd interrupted his routine for her. Sheldon noticed her look of astonishment and said, "Watching the Doctor and the Ponds save the universe wouldn't feel the same without you."

Penny smiled. "And hating on River." They both agreed Rose was much better suited for the Doctor and hated River with a passion.

Sheldon nodded. "We'll watch it later. But you don't have to leave yet."

Penny smiled. "Okay, sweetie. I don't have work today."

The three of them chatted for a while, until Mary left to do some shopping. Sheldon started Doctor Who and they watched as the Ponds and the Doctor worked to get out of the Dalek asylum.

Penny decided to experiment again. She took Sheldon's hand. He didn't pull back. He put his arm around her and pulled her close.

Penny froze. Sheldon was snuggling with her. Again. This was still really weird. She glanced up at the physicist. He was focused on the show and she looked back at the screen. The show ended and Penny grinned. That had been a good episode.

"It's nice how much Amy and Rory love each other." Penny said.

"I suppose." Sheldon replied.

"I wish someone loved me enough to wait two thousand years for me. Or loved me enough to burn up a sun just to say goodbye" Penny said without thinking.

Sheldon muttered something and Penny could have sworn he said, "I do."

"Did you just say you do?" Penny asked quietly.

Sheldon blushed and whispered, "Maybe."

Penny couldn't take it anymore. She leaned in and kissed Sheldon. He kissed her back, putting his other arm around her. It was a sweet kiss, no tongue or anything, but passionate.

Sheldon pulled back. "Penny, I... I love you."

Penny grinned. "I love you too, Sheldon."

**Author's Note: Sorry if you don't understand the Doctor Who references in this chapter. I couldn't resist putting a few in since I am a huge Whovian! If you did understand them, yes I made them Rose/Doctor shippers and River haters because that's what I am. Anyway, I have a question that only you can answer. Should I continue with this? Tell me in your reviews!**


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